Hatcheries have been increasingly asked to contribute to conserving natural salmon populations, as well as to continue to produce fish to mitigate for lost harvest opportunities. A key biological uncertainty about the effects of hatchery production on natural populations is the degree to which hatchery produced fish can reproduce in the natural environment. In order to assess the impact (positive or negative) of naturally spawning hatchery fish we are using a DNA-based pedigree analysis to directly measure the relative reproductive success of hatchery and natural-origin salmon in streams various streams in the Pacific Northwest.
These projects take advantage of advanced genetic technology that allows for rapid screening of thousands of individuals at multiple highly variable genetic markers to determine how many progeny are produced by individual natural-origin and hatchery-origin fish when they spawn together in the same natural stream. The basic approach is illustrated in Figure 1: adult salmon are sampled as they return upstream to spawn. At the time of sampling, the origin (hatchery or natural) of each fish is determined, measurements such as length are made, and a small tissue sample (fin clip) is collected for genetic analysis. The fish are then allowed to either proceed upstream, or in some cases are taken into a hatchery to be spawned. Offspring from these potential spawners are then collected at various life stages (fry/parr, smolt, adult), and genetically sampled. Statistical methods are then used to determine which of the sampled spawners produced which progeny. The number of progeny a fish produces is a measure of its fitness, and comparisons of fitness across groups (e.g., hatchery versus natural origin) can be made based on the progeny counts for the group members.